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Saturday, April 18, 2020

Three scientists discuss junk DNA

I just found this video that was posted to YouTube on May 2019. It's produced by the University of California and it features three researchers discussing the question, "Is Most of Your DNA Junk!" The three scientists are:
  • Rusty Gage, a neuroscientist at the Salk Institute
  • Alysson Muotri, who studies brain development at the University of California, San Diego
  • Miles Wilkinson, who studies neuronal and germ cell development at the University of San Diego
None of them appear to be experts on genomes or junk DNA although one of them (Wilkinson) appears to have some knowledge of the evidence for junk DNA, although many of his explanations are garbled. What's interesting is that they emphasize the fact that some transposon-related sequences are expressed in some cells and they rely on this fact to remain skeptical of junk DNA. They also propose that excess DNA might be present in order to ensure diversity and prepare for future evolution. All three seem to be comfortable with the idea that excess DNA may be protecting the rest of the functional genome.

This is a good example of what we are up against when we try to convince scientists that most of our genome is junk.





52 comments :

  1. 1:30 in, one guy says Junk DNA is defined as DNA having "no selective value."

    Should I stop watching right there?

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  2. "All three seem to be comfortable with the idea that excess DNA may be protecting the rest of the functional genome".

    Dan Graur is not happy with that.

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    1. I don't know how you interpreted it, but what I was trying to say is that Dan would be unhappy, cuz he already wrote a comment "On the Imbecilic Claim that Junk DNA Protects Functional DNA from Mutations" where he shows why this is bad argument.

      Here: https://judgestarling.tumblr.com/post/188325575781/on-the-imbecilic-claim-that-junk-dna-protects#disqus_thread

      I am with you and Dan! I'm gonna read what you linked. Thank you.

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    2. I interpreted your comment correctly. I just wanted to point out that lots of other people have been pointing out the silliness of insulation theory for the past 40 years or more. I have been unhappy about it for about 25 years.

      See The "Insulation Theory of Junk DNA" for a brief discussion of the part that Dan ignores.

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    3. Thank you so much, Larry! I've been learning a lot with you here. Really enjoyed your both posts on the issue. I wonder if you'll have pages to discuss this and so many other things in "What's in your genome".

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  3. Can I say that "all DNA is functional, there is no junk DNA" is genomic flat-earth?

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  4. Lynch has put out 5 chapters form his upcoming book "The Origins of Cellular Architecture" (https://michael-lynch.webnode.com/), in the first chapter he talks about the EES and about some objections to the neutral theory (by Hahn), I'd like to hear your thoughts about it.

    Also how is your book going?

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    1. I think everyone should read Lynch's book. I agree with almost everything he writes and I love the way he writes it. Here's his final word on EES proponents.

      In summary, although those who promote the need for an urgent overthrow of current evolutionary theory are unlikely to read the preceding comments, we offer them primarily for the benefit of outsiders with only a peripheral understanding of what might appear to be a meaningful controversy.

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  5. The first speaker at least allows that the transcriptional activity from this excess DNA does not seem functioning. But he asserts that the other 99% of the human genome that does not code for protein is described as junk DNA. Well, a simple pie chart that summarizes what is in our genome shows otherwise. The 2nd speaker also makes errors, but he does propose that at least some of this excess DNA, generated as junk, may have been preserved because of it was recruited into a function in the past, but that function has since been lost. Its an idea worth considering, but this DNA has the appearance of non-functioning DNA and that is the better hypothesis right now.

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  6. You have made Uncommon Descent unhappy. See their post on "Larry Moran’s uphill battle convincing scientists that most of the genome is junk DNA" They also say that "ASU’s Michael Lynch’s new book takes aim at “natural selection” as a sum total explanation"

    Other catchy titles are "Must historians exclude claims about miracles?" and " Moving beyond COVID crazy: Is there evidence for Jesus’s resurrection?"
    So religion has nothing to do with ID. Good to know.

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    1. "as a sum total explanation" is quite a straw man position. As if evolutionary biologists refuse to acknowledge any role for other processes such as genetic drift.

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    2. You expect anything from ID liars

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    3. Leave it UD to keep bringing the crazy

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  7. It shouldn't be there, should it?

    https://phys.org/news/2020-02-cartilage-cells-chromosomes-dna-million-year-old.html

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    1. The authors detected the presence of DNA in a few cells from extremely well-preserved soft tissue of a 75 million-year-old dinosaur, The DNA was detected by staining, which simply requires the presence of some double-stranded DNA.

      I don't see any reason to doubt the results. Under the right conditions small bits of DNA could be preserved for millions of years.

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    2. 75 million years. I guess under the right conditions, cows really can jump over the moon.

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    3. Well, as a paleontologist who thinks this thing does not disprove an old Earth, I should say that it seems you didn't read the paper. The authors of the paper are very cautious. They don't claim have found intact DNA. Read the paper.

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    4. This comment has been removed by the author.

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    5. *you have to be...

      Well, typos, typos... Typos everywhere!

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    6. Correcting some typos:

      "This not only supports that the compound within these cells is *chemically consistent with DNA*, but that material is double stranded, and of a *minimum length of 6 base pairs*".

      "This study provides the first clear chemical and molecular demonstration of calcified cartilage preservation in Mesozoic skeletal material, and suggests that in addition to cartilage-specific collagen II, DNA, or at least the *chemical markers of DNA* (for example, chemically altered base pairs that can still react to PI and DAPI), may preserve for millions of years."

      Anyway. If molecules such as DNA can live longer than we previously thought, this means that.... if the right conditions are met, molecules such as DNA can live longer than we previously thought.

      You have to bo either ignorant or small-minded to think that such study supports YEC.

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    7. "75 million years. I guess under the right conditions, cows really can jump over the moon."

      Yeah and let's not get started on the talking snakes and men walking on water.

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    8. But you like top-shelf miracles. How many random DNA replication errors would you suppose it took to get this to work?

      https://www.smithsonianmag.com/science-nature/this-insect-has-the-only-mechanical-gears-ever-found-in-nature-6480908/

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    9. Oh gee you can't figure it out, so magic man musta done it.

      Look, the trait is heritable, hence it is encoded in genes, and those are evolvable entities. As are species, including the one that carries it. Hence the trait evolved.

      If you want to know how, you'd have to study a whole host of closely related insects to determine what morphological structures they have that might be similar to this one, derive a phylogeny that would allow you to trace it's evolution, and then ultimately you'd have to look into the genetic and developmental pathways responsible for producing the trait. Then you'd have your answer. Here's who is never going to find out: Creationist crackpots who think the answer is God-magic when they can't figure it out.

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    10. "Look, the trait is heritable, hence it is encoded in genes"

      No. Once upon a time, there were no genes to code for the very specialized folded proteins necessary for functional gears. Accidents cannot produce such genes.

      You have lots of very nice convoluted double-talk going on there. But there are no developmental pathways in unguided processes. Random means random. You haven't figured anything out at all.

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    11. "No."

      Sorry, but yes. If the insect has these, and it's offspring does too, then it is a heritable trait and is encoded in the heritable material. That would be it's genes.

      "Once upon a time, there were no genes to code for the very specialized folded proteins necessary for functional gears. Accidents cannot produce such genes."

      .. he declared, with great conviction. But that was all he was doing. Of course, there is no evidence that any proteins that partake in the structure of these gears are novel and had to evolve anew for the gears to evolve. It could just as well be changes in localized expression of chitin and sclerotin(you know, the materials insect exoskeletons are primarily made of). That implies changes in localized gene regulation, as in when and where and how much of this material is produced in order to produce these gears.

      "You have lots of very nice convoluted double-talk going on there."

      No I'm actually explaining to you what it would take to answer your first question, about how many mutations it would take to evolve a trait like this.

      "But there are no developmental pathways in unguided processes. Random means random."

      Ahh I see you're a complete igoramus of biology, and you are confusing evolution(transgenerational change in populations of organisms) with developmental biology. To understand how the trait evolved (the evolution part, aka the "random mutation+natural selection and genetic drift" stuff) you would have to determine the genetics encoding it, and to do that you would have to study it's development and trace the changes in development to expression of particular genes. And you'd have to do that both for this insect, and for it's close relatives, to see how the underlying genetics have changed and what results this had on morphology.

      Morphological traits in multicellular organisms (such as these gears in insects) are encoded in genes, and are due to how the organism develops from the zygote state following fertilization.
      https://en.wikipedia.org/wiki/Developmental_biology.

      You haven't figured anything out at all.

      No, that's why I'm telling you what it would take to do that. Work that no creationist will ever bother doing, because they're not actually interested in the science of biology, only to evangelize for their pseudoscientific ID-creationist cult. To them, these gears are just a tool to try to shove their trash religion down other people's throats, they couldn't give a damn about trying to understand how the world actually works.

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    12. "how the trait evolved (the evolution part, aka the "random mutation+natural selection and genetic drift" stuff) you would have to determine the genetics encoding it, and to do that you would have to study it's development and trace the changes in development to expression of particular genes"

      Horsefeathers. You're overlooking very scientific principles:

      Random accidents cannot produce organized, functional, integrated systems. Believe whatever you like, but that is the real-life truth in this universe.

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    13. I guess txpiper has never heard of natural selection, and so thinks that evolutionary processes are "random accidents". Of course the words "organized, functional, integrated" are there to give txpiper the wiggle room to cope with any example we give, by saying that the example is not "organized, functional, integrated". So this is the same creationist nonsense we have seen many times before.

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    14. Natural selection is a removal process. It does not cause miraculous mutations to occur and reoccur until something biological is up and running.

      How exactly would natural selection be involved in the supposed development of the gear arrangement mentioned above?

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    16. Natural selection is a removal process.

      Common creationist gotcha, and a misguided one at that. Populations typically produce an excess of offspring, and some are killed off (or prevented from reproducing) by a scarcity of resources, or by other density-dependent population size regulation processes. The result is that one genotype being selected against goes hand in hand with the other genotypes having an increased probability of survival and reproduction. So it is not just "a removal process". You've been misled.

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    17. "The result is that one genotype being selected against goes hand in hand with the other genotypes having an increased probability of survival and reproduction."

      Oh, yes. The other genotypes are 'selected for'. But in reality, nothing is actually being selected at all. Genotypes able to cope with their environment survive, and those that cannot don't survive. Selection is just what happens. It isn't a universal ethereal force, and it sure as hell isn't a fairy with multiple personalities.

      That aside, what makes you think that random DNA replication errors occurred and reoccurred till functional systems like gears, or kidneys or eyes or bioluminescence were built? What actual scientific discovery suggests that things like that happened countless millions of times? If you were in front of an auditorium full of bright students, and someone asked you those questions, what would you say?

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    18. You have not shown that there is some limit of adaptation that cannot be exceeded. The person who declares that there is such a limit, well, they have to show why. Personal incredulity doesn't count -- show us a mathematical result. William Dembski turned out not to have such a proof (the infamous 500-bit criterion for detecting Design). Have heard nothing like that from txpiper.

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    19. I can't prove that Elvis is not running a fusion bar on Saturn, either. But you are the one making the extraordinary claims. You should be showing your evidence, not declaring your beliefs.

      sci·en·tif·ic meth·od
      noun
      a method of procedure that has characterized natural science since the 17th century, consisting in systematic observation, measurement, and experiment, and the formulation, testing, and modification of hypotheses.

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    20. I did a word search on this article for 'mutation', but it wasn't mentioned in this one. Ir rarely is. That's curious since mutations are supposed to the actual operative centerpiece for evolution.

      I keep looking for someone willing to step up to the plate and explain how random DNA copy errors actually result in miraculous biological sophistication, but nobody is interested in doing that. I can understand that. It doesn't take long to recognize the staggering problems involved. What I don't understand is why people accept such a preposterous idea on faith.

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    21. "I did a word search on this article for 'mutation', but it wasn't mentioned in this one."

      Then you're incompetent, since mutation is in fact mentioned many times in the article. In part 1, part 2, part 4, and part 5. You understand how links work right? You click them, and then you read what they say, besides just brainlessly doing word-searches.

      "I keep looking for someone willing to step up to the plate and explain how random DNA copy errors actually result in miraculous biological sophistication, but nobody is interested in doing that."

      That's because it so simple and obvious one has to wonder why that should even be necessary. The system of inheritance intrinsically lends itself to gradual, step-wise evolutionary change, given it’s basis in a digital polymer.

      Heck, we even know of all the types of mutations that are possible, which are basically all the change, copy, insert, and rearrangement-tools one could imagine would be necessary for the function for an incrementally changing system of polymer sequences.

      It’s almost like genetics is exactly the kind of thing that enables and facilitates the slow gradual process of trans-generational evolutionary change, whereby in splitting populations of organisms, the independent accumulation of genetic mutations with their changing effects on phenotype are subject to natural selection.

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    22. “mentioned many times in the article. In part 1, part 2, part 4, and part 5.”

      Yes, in the sub-sections, but not in any developmental context. Lethality, background rates, abnormalities, how genes became pseudogenes, etc., but nothing to do with the evolution of novel features or systems.

      ==

      “why [explanations] should even be necessary”

      Because they are so lacking. A lot is known about mutations. Their actual effects are enshrined in disease databases. What is not known is how in hell they could possibly produce functional biological features, organs and systems.

      ==

      “The system of inheritance intrinsically lends itself to gradual, step-wise evolutionary change, given it’s basis in a digital polymer.”

      Well, no. Because there is nothing intrinsic about random errors.

      ==

      “we even know of all the types of mutations that are possible…basically all the change, copy, insert, and rearrangement-tools”

      They are all ways to do nothing, or to ruin something. Multiple types only complicate the problem. Any old mutation won’t do in an accidentally developing system.

      May I ask, are you aware of any unfinished specialties? Something still under evolutionary construction? Waiting for those last few errors to happen?

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    23. "They are all ways to do nothing, or to ruin something."

      If a mutation can ruin something, a mutation can construct it. Put the "ruined" state as ancestral, and then have the reverse mutation occur, and you've got the construction. Simple.

      If AAGCT has no function but AACCT does, then AAGCT mutating into AACCT creates the function (by the substitution of G for C). This is why your question is so unfathomably inane, as the solution is straightforwardly obvious.

      "Multiple types only complicate the problem."

      That's like saying that having the cut/copy and paste function in your text editor, in addition to the letter keys, makes it harder to create new text. Obviously nonsensical. The ability to copy, translocate, and recombine, in addition to substitutions, insertions, and deletions, actually speeds up evolution under many circumstances, than if only single substitutions were allowed.

      "Any old mutation won’t do in an accidentally developing system."

      And yet countless examples are known of combinations of mutations that yield novel functions. For example, De Novo Emergence of Peptides That Confer Antibiotic Resistance.

      "May I ask, are you aware of any unfinished specialties? Something still under evolutionary construction? Waiting for those last few errors to happen?"

      You mean besides your brain? The Bsc4 protein in yeast, which exhibits all the hallmarks of a young functional protein coding gene still evolving under natural selection into a protein with a stable globular fold. Besides that, countless species of aquatic and semi-aquatic mammals(look at the limbs of otters, sea-otters, platupuses, seals, sea-lions, walruses, sea-cows, manatees, hippos, and so on ad infinitum). Not to mention gliding squirrels, gliding snakes, mudskippers, handfish, etc. etc. And then there are the Kings of looking like an unfished product: Flatfish. Amazingly, they develop embryonically like "normal" fish to begin with, with one eye on each side of the head, but then one the eyes gradually migrates to the other side of the head during embryonic development.

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    24. If you can look at those gears and see random events, and if you believe the stuff Dr. Bailleul found in the skull fragments is 75 million years old, then your perception of the world is just different than mine. I think this is what Malcom Muggeridge was noticing: "We have educated ourselves into imbecility."

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    25. Ahh yes, education, that age old enemy of superstition.

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    26. Maybe education is the wrong word. If you're having your nose rubbed in evidence and can't notice it, maybe you've just been trained.

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    27. Ancient muscle tissue extracted from 18 million year old fossil

      https://phys.org/news/2009-11-ancient-muscle-tissue-million-year.html

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    28. Long-term preservation of organic material under special circumstances is an exciting new field. Turns out what we once thought we knew about preservation was incomplete, and that under the right circumstances such material can last much longer than first assumed.

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    29. Over three decades ago Jerrold Lowenstein of San Francisco State University ground up material from the fossil Ramapithecus, about 15 million years old, and injected it into a rabbit. The antibodies elicited showed strongest reaction with orangutang, suggesting that Ramapithecus and orangs were a clade. It implied that there was residual protein still present after almost 15 million years. In his sensitive radioimmunoassay, other fossils millions of years old also showed evidence of immunologically detectable collagen.

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    30. "such material can last much longer than first assumed"

      Yeah, that was a piss-poor taphonomic assumption. They are more enlightened and liberated now. DNA replication errors were apparently busy producing cholesterol-bearing animals before that Cambrian.

      “It’s part of a renaissance in the field in palaeontology,” said Gold. “We’re discovering, as our tools and technologies get better and better, we’re finding that actually there are all sorts of organic matter — proteins, fats, different carbon compounds — things that we didn’t think could survive for such a long period of time,” he added.

      “Because of that we can find things like preserved pigments to see the colours of dinosaurs, or in this case, the cholesterol content of 500-million-year-old fossil.”

      https://www.news.com.au/technology/science/evolution/a-558millionyear-riddle-and-a-global-palaeontology-feud-has-been-settled/news-story/11079e877385afb1620adcb008dc8c53

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    31. Correction: Jerrold Lowenstein was at UCSF, not SFSU.

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    32. Nobody has a frame of reference for millions of years. It's just words, disconnected from reality and science.

      "Here we report evidence of protein preservation in a terrestrial vertebrate found inside the vascular canals of a rib of a 195-million-year-old sauropodomorph dinosaur, where blood vessels and nerves would normally have been present in the living organism."
      https://www.nature.com/articles/ncomms14220

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    33. "Maybe education is the wrong word. If you're having your nose rubbed in evidence and can't notice it, maybe you've just been trained."

      You owe everyone new irony meters after that piper.

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  8. "Natural selection is a removal process."

    You're thinking of negative or so-called purifying selection, where deleterious changes are selected against, instead of positive selection where beneficial changes are increased in frequency.

    "How exactly would natural selection be involved in the supposed development of the gear arrangement mentioned above?"

    Ahh the classic appeal to ignorance, "but how would..?"

    To answer that question you would have to start by considering how closely related insects without these gears move their legs, what forces and mechanisms are involved, how they are genetically encoded, and in what way mutations affect the morphology and function of the legs on these insects. What are the magnitudes of selective pressures involved, and so on.

    A guess I have is that on related insects without these gears, their legs nevertheless push against each other and produce mutual friction, by implication their common ancestor did too. (a similar but more rudimentary gear-like structure is seen in mandibles in other species of insect, where friction between them helps synchronize the pincer movement of both mandibles)

    In the same way, the friction generated between the legs unavoidably transfers torque from one leg to the other(ineffectively compared to those with true gears). If increases in this transfer of torque is beneficial, and if mutations are capable of altering the amount of friction, natural selection has the potential to incrementally increase the friction generated if increased synchronization is beneficial.
    Tiny variations in lumpiness creates traction, which is increased friction. It’s pretty easy to see how the tiny lumps deriving from small variants in chitin expression by underlying cells could grow bigger by localized increased expression in chitin(possibly just pointing to a handful of regulatory mutations), culminating in the gears we see today.

    So that's just one way that could happen in principle.

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